Research workbench
Crystal structure of yeast thiamin pyrophosphokinase
Analyse Crystal structure of yeast thiamin pyrophosphokinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IG0
- Type
- protein
- Length
- 636 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiamin pyrophosphokinase
- EC
- 2.7.6.2
- UniProt
- P35202
- Ligands
- VIB
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thiamin pyrophosphokinase (EC 2.7.6.2) | protein | 317 | 32% helix, 30% strand | P35202 |
| B | Thiamin pyrophosphokinase (EC 2.7.6.2) | protein | 319 | 34% helix, 30% strand | P35202 |
Ligands and binding sites
- VIB · 3-(4-amino-2-methyl-pyrimidin-5-ylmethyl)-5-(2-hydroxy-ethyl)-4-methyl-thiazol-3-ium · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 607 | 0.71 | 0.79 | 66 | VIB |
| 2 | 603 | 0.69 | 0.78 | 71 | VIB |
| 3 | 255 | 0.67 | 0.83 | 27 | empty |
| 4 | 250 | 0.63 | 0.81 | 24 | empty |
| 5 | 127 | 0.55 | 0.82 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1642 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P35202
- Elsewhere: RCSB PDB 1IG0 · PDBe 1IG0 · UniProt P35202
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